As pointed out in https://bugs.meego.com/show_bug.cgi?id=25562 the initial IPv6 setup on syncevolution.org did not work (some kind of SSL certificate issue when used over IPv6). Therefore the IPv6 address of syncevolution.org was removed from DNS again, as a short term workaround (not a pressing issue, though, so short term can become pretty long).
Need to figure out what the problem was and fix it properly. It would be interesting to know whether https://01.org has the same problem - it uses a similar setup.
Curl via a proxy which uses IPv6 seems happy now:
* Server certificate:
* subject: OU=Domain Control Validated; OU=Issued through Intel Corporation E-PKI Manager; OU=COMODO SSL; CN=syncevolution.org
* start date: 2013-11-22 00:00:00 GMT
* expire date: 2016-11-21 23:59:59 GMT
* subjectAltName: syncevolution.org matched
* issuer: C=GB; ST=Greater Manchester; L=Salford; O=COMODO CA Limited; CN=COMODO SSL CA
* SSL certificate verify ok.
Closing the issue.